Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing

Chen, Shanlan; Mo, Yujian; Zhang, Yingjie; Zhu, Hongbao; Yu, Lexiang

doi:10.1007/s00425-022-03965-5

Cited by 5 publications

(4 citation statements)

References 62 publications

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“…Moreover, AS regulations of homologous GR-RBPa genes changed significantly among different plant species, and no clear divergence of AS regulation model was found between monocot and dicot species. These findings highlight the complexity and variability of AS regulations in coding genes of the RNA binding proteins (RBPs), which have also been recently reported in another family, serine/arginine-rich (SR) protein 45 , 69 .…”

Section: Discussionsupporting

confidence: 67%

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Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress

Zhang,

Mo,

et al. 2024

Sci Rep

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The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.

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Section: Discussionsupporting

confidence: 67%

“…To further investigate the expression patterns of GR-RBPa genes at the post-transcriptional level, we utilized AS detection RT-PCR, a method previously established 45 . According to the results, all 13 genes in branch I underwent AS, even under normal conditions (Fig.…”

Section: Resultsmentioning

confidence: 99%

Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress

Zhang,

Mo,

et al. 2024

Sci Rep

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“…Heat stress caused substantial disturbances in both gene transcription and pre-mRNA AS. Tissue-and species-specific AS regulations in response to stresses were noted in sweet potato, unlike Arabidopsis and rice [206].…”

Section: Abiotic Stress Adaptationmentioning

confidence: 95%

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

Dwivedi,

Quiroz,

Reddy

et al. 2023

IJMS

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Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.

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“…Reverse transcription-PCR (RT-PCR) and reverse transcriptionquantitative PCR (qRT-PCR) were slightly modified compared with the methods previously described in (Chen et al, 2022). DNA digestion of total RNA samples was performed after RNA extraction by using an RNase-Free DNase Set (Vazyme, Catalog No.…”

Section: Qrt-pcr and Rt-pcrmentioning

confidence: 99%

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

Li²,

Liu³

et al. 2023

Front. Plant Sci.

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Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.

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Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing

Cited by 5 publications

References 62 publications

Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress

Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

OsGRF4AA compromises heat tolerance of developing pollen grains in rice

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